Figures for White et al. 2017
Richard White
24th January 2017
Fig. 1b
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Fig 1c
Genes detected
Fig 1d
Sample Correlation Matrix
Fig 1e-h
PCA Plots (using all genes)
3d plot
PC Median Heatmaps
Figure 1-1
Distribution of mean TPM by stage
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Figure 1-2
PCA Matrix Plot
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DETCT Sample QC plot
Figure 1-4
DETCT PCA
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Fig3A
Max Stage Clusters TPM heatmap
ZFA enrichment
Figure 3-1
Orthologues of Named/Unnamed genes
Named Genes
Unnamed Genes
Figure 3-2
Effect of Normalisation on cluster 11
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Figure 4
| Cluster | Chromosome | Count | Expected | log2FE | Adjusted.pvalue |
|---|---|---|---|---|---|
| Cluster023 | Chr1 | 9 | 2.25 | 2.00 | 1.161e-02 |
| Cluster004 | Chr4 | 129 | 47.29 | 1.45 | 7.434e-24 |
| Cluster022 | Chr4 | 14 | 5.03 | 1.48 | 1.156e-02 |
| Cluster037 | Chr4 | 23 | 3.35 | 2.78 | 9.033e-14 |
| Cluster084 | Chr4 | 9 | 1.48 | 2.61 | 1.659e-04 |
| Cluster074 | Chr12 | 8 | 0.48 | 4.05 | 6.337e-07 |
Table showing clusters with significant chr enrichments (adjusted p-value < 0.05 and log2 fold change > 1).
Chr 4 Zinc Finger Genes
| Cluster | Freq | |
|---|---|---|
| 4 | Cluster004 | 120 |
| 37 | Cluster037 | 18 |
| 22 | Cluster022 | 14 |
| 84 | Cluster084 | 6 |
Table showing the numbers of chromosome 4 zinc finger genes in the biolayout clusters (more than 5 in a cluster).
Chr 4 ZnF enrichment
The table below shows the clusters with enrichments significantly larger than expected by chance for the chromosome 4 zinc finger genes.
| Cluster | Category | Count | Expected | log2FE | pvalue | adjusted.pvalue |
|---|---|---|---|---|---|---|
| Cluster004 | Chr4ZnF | 120 | 7.87 | 3.93 | 1.203e-101 | 6.015e-101 |
| Cluster022 | Chr4ZnF | 14 | 0.84 | 4.06 | 7.471e-14 | 3.735e-13 |
| Cluster037 | Chr4ZnF | 18 | 0.56 | 5.01 | 1.270e-23 | 6.349e-23 |
| Cluster084 | Chr4ZnF | 6 | 0.25 | 4.61 | 8.588e-08 | 4.294e-07 |
Table showing clusters with significant enrichments (adjusted p-value < 0.05).
Fig4A
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## 2Fig4C - NLR genes tpm heatmap
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## 2Fig4D - Chr22 Znf genes tpm heatmap
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## 2Fig4E - Chr4 tpm heatmap
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## 2Fig4F-G - histograms of ZnF/NLR genes on chr 4
Histogram showing the distribution of genes in clusters 4, 22, 37 and 84.
Histogram showing the distribution of NLR genes on chromosome 4 (binwidth = 5 Mb).
Figure 4-2
histograms of ZnF genes on chr 4, split by cluster
Histogram showing the distribution of genes in clusters 4, 22, 37 and 84, split by cluster.
Regional expression
Figure 4-3A
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Figure 5
Fig5A
Pearson histogram (Paralogues)
Histogram of Pearson coefficients between paralogous gene pairs (binwidth = 0.1)
Fig5B
Pearson histogram (random sample)
Histogram of Pearson coefficients of a random selection of 3000 genes pairs.
Fig5C
top10/bottom10 tpm heatmap
Fig5D-G
scatterplots/point based expression profiles
Fig.6C
Count bar chart by Stage
Session Info
## R version 3.3.1 (2016-06-21)
## Platform: x86_64-apple-darwin13.4.0 (64-bit)
## Running under: OS X 10.11.6 (El Capitan)
##
## locale:
## [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
##
## attached base packages:
## [1] grid stats4 parallel stats graphics grDevices utils
## [8] datasets methods base
##
## other attached packages:
## [1] rgl_0.97.0 qvalue_2.4.2
## [3] genefilter_1.54.2 DESeq2_1.12.4
## [5] SummarizedExperiment_1.2.3 htmlTable_1.9
## [7] biomaRt_2.28.0 Rgraphviz_2.16.0
## [9] gridExtra_2.2.1 topGO_2.24.0
## [11] SparseM_1.7 GO.db_3.3.0
## [13] graph_1.50.0 cba_0.2-18
## [15] proxy_0.4-16 RColorBrewer_1.1-2
## [17] plyr_1.8.4 GenomicFeatures_1.24.5
## [19] AnnotationDbi_1.34.4 Biobase_2.32.0
## [21] GenomicRanges_1.24.2 GenomeInfoDb_1.8.3
## [23] IRanges_2.6.1 S4Vectors_0.10.3
## [25] BiocGenerics_0.18.0 scales_0.4.1
## [27] reshape2_1.4.2 ggplot2_2.1.0
## [29] rprojroot_1.2 knitr_1.15.1
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## loaded via a namespace (and not attached):
## [1] jsonlite_1.0 splines_3.3.1
## [3] shiny_1.0.0 Formula_1.2-1
## [5] highr_0.6 latticeExtra_0.6-28
## [7] Rsamtools_1.24.0 yaml_2.1.14
## [9] RSQLite_1.1-2 backports_1.0.5
## [11] lattice_0.20-34 digest_0.6.12
## [13] XVector_0.12.1 checkmate_1.8.1
## [15] colorspace_1.2-6 httpuv_1.3.3
## [17] htmltools_0.3.5 Matrix_1.2-6
## [19] XML_3.98-1.5 zlibbioc_1.18.0
## [21] xtable_1.8-2 BiocParallel_1.6.6
## [23] annotate_1.50.0 nnet_7.3-12
## [25] mime_0.5 survival_2.40-1
## [27] magrittr_1.5 memoise_1.0.0
## [29] evaluate_0.10 foreign_0.8-66
## [31] tools_3.3.1 data.table_1.10.0
## [33] matrixStats_0.50.2 stringr_1.1.0
## [35] munsell_0.4.3 locfit_1.5-9.1
## [37] cluster_2.0.5 Biostrings_2.40.2
## [39] RCurl_1.95-4.8 htmlwidgets_0.8
## [41] labeling_0.3 bitops_1.0-6
## [43] base64enc_0.1-3 rmarkdown_1.3
## [45] gtable_0.2.0 DBI_0.5-1
## [47] R6_2.2.0 GenomicAlignments_1.8.4
## [49] rtracklayer_1.32.2 Hmisc_4.0-2
## [51] stringi_1.1.1 Rcpp_0.12.9
## [53] geneplotter_1.50.0 rpart_4.1-10
## [55] acepack_1.4.1